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1
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84866000072
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We employ the word structural in the same context as its usage in dynamical systems literature on structural stability. The word susceptibility is inspired from physics wherein it is a measure of response to a perturbation (such as an applied external field) quantified by the second derivative of the free energy with respect to parameters. Since cost is analogous to free energy (in that both are minimized), it is natural to refer to the response to perturbations in dynamics, also quantified via second derivatives, as structural susceptibility.
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We employ the word structural in the same context as its usage in dynamical systems literature on structural stability. The word susceptibility is inspired from physics wherein it is a measure of response to a perturbation (such as an applied external field) quantified by the second derivative of the free energy with respect to parameters. Since cost is analogous to free energy (in that both are minimized), it is natural to refer to the response to perturbations in dynamics, also quantified via second derivatives, as structural susceptibility.
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2
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85035221677
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PLEEE8 1539-3755 10.1103/PhysRevE.68.021904
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K. S. Brown and J. P. Sethna, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.68.021904 68, 021904 (2003).
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(2003)
Phys. Rev. e
, vol.68
, pp. 021904
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Brown, K.S.1
Sethna, J.P.2
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3
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35748977901
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Universally sloppy parameter sensitivities in systems biology models
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DOI 10.1371/journal.pcbi.0030189
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R. N. Gutenkunst, J. J. Waterfall, F. P. Casey, K. S. Brown, C. R. Myers, and J. P. Sethna, PLoS Comput Biol 1553-734X 10.1371/journal.pcbi.0030189 3, e189 (2007). (Pubitemid 350043403)
-
(2007)
PLoS Computational Biology
, vol.3
, Issue.10
, pp. 1871-1878
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Gutenkunst, R.N.1
Waterfall, J.J.2
Casey, F.P.3
Brown, K.S.4
Myers, C.R.5
Sethna, J.P.6
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5
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34249744604
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Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model
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DOI 10.1049/iet-syb:20060065
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F. P. Casey, D. Baird, Q. Feng, R. N. Gutenkunst, J. J. Waterfall, C. R. Myers, K. S. Brown, R. A. Cerione, and J. P. Sethna, IET Syst. Biol. 1751-8849 10.1049/iet-syb:20060065 1, 190 (2007). (Pubitemid 46831213)
-
(2007)
IET Systems Biology
, vol.1
, Issue.3
, pp. 190-202
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Casey, F.P.1
Baird, D.2
Feng, Q.3
Gutenkunst, R.N.4
Waterfall, J.J.5
Myers, C.R.6
Brown, K.S.7
Cerione, R.A.8
Sethna, J.P.9
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6
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36248970060
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Extracting falsifiable predictions from sloppy models
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DOI 10.1196/annals.1407.003, Reverse Engineering Biological Networks: Opportunities and Challenges in Computational Methods for Pathway Inference
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R. N. Gutenkunst, F. P. Casey, J. J. Waterfall, C. R. Myers, and J. P. Sethna, Ann. N.Y. Acad. Sci. ANYAA9 0077-8923 10.1196/annals.1407.003 1115, 203 (2007). (Pubitemid 350134793)
-
(2007)
Annals of the New York Academy of Sciences
, vol.1115
, pp. 203-211
-
-
Gutenkunst, R.N.1
Casey, F.P.2
Waterfall, J.J.3
Myers, C.R.4
Sethna, J.P.5
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8
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77956498018
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-
1742-206X 10.1039/b918098b
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J. F. Apgar, D. K. Witmer, F. M. White, and B. Tidor, Mol. BioSyst. 1742-206X 10.1039/b918098b 6, 1890 (2010).
-
(2010)
Mol. BioSyst.
, vol.6
, pp. 1890
-
-
Apgar, J.F.1
Witmer, D.K.2
White, F.M.3
Tidor, B.4
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10
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59049098884
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1553-734X 10.1371/journal.pcbi.1000256
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A. Dayarian, M. Chaves, E. D. Sontag, and A. M. Sengupta, PLoS Comput Biol 1553-734X 10.1371/journal.pcbi.1000256 5, e1000256 (2009).
-
(2009)
PLoS Comput Biol
, vol.5
, pp. 1000256
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-
Dayarian, A.1
Chaves, M.2
Sontag, E.D.3
Sengupta, A.M.4
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11
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80052337295
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1553-734X 10.1371/journal.pcbi.1002130
-
H. Hettling and J. H. G. M. van Beek, PLoS Comput Biol 1553-734X 10.1371/journal.pcbi.1002130 7, e1002130 (2011).
-
(2011)
PLoS Comput Biol
, vol.7
, pp. 1002130
-
-
Hettling, H.1
Van Beek, J.H.G.M.2
-
15
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-
0003490410
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Westview, Boulder, CO
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S. H. Strogatz, Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry and Engineering (Westview, Boulder, CO, 2001).
-
(2001)
Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry and Engineering
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-
Strogatz, S.H.1
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16
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53349102813
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Incidentally, the set of equations can also be considered to be a special case of the FitzHugh-Nagumo model [see R. FitzHugh, Biophys J. 1, 445 (1961)] introduced three decades later as a simplification of the Hodgkin-Huxley equations of neuronal spikes in the squid giant axons, and is sometimes referred to as the Bonhoeffer-van der Pol model.
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Incidentally, the set of equations can also be considered to be a special case of the FitzHugh-Nagumo model [see R. FitzHugh, Biophys J. 1, 445 (1961)] introduced three decades later as a simplification of the Hodgkin-Huxley equations of neuronal spikes in the squid giant axons, and is sometimes referred to as the Bonhoeffer-van der Pol model.
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18
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0003478288
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Springer, New York, NY
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J. M. Guckenheimer and P. Holmes, Nonlinear Oscillations, Dynamical Systems and Bifurcations of Vector Fields (Springer, New York, NY, 1983).
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(1983)
Nonlinear Oscillations, Dynamical Systems and Bifurcations of Vector Fields
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Guckenheimer, J.M.1
Holmes, P.2
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20
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84866000073
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Perturbations distort the dynamics so that the attractor and its period change. We addressed these issues by setting the periods to unity, and by moving the initial conditions to the new attractor to remove any transients. Alternatively, if we fit data over many periods without making the said changes, the parameter combinations determining the period and phase would become stiff modes in our dynamics.
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Perturbations distort the dynamics so that the attractor and its period change. We addressed these issues by setting the periods to unity, and by moving the initial conditions to the new attractor to remove any transients. Alternatively, if we fit data over many periods without making the said changes, the parameter combinations determining the period and phase would become stiff modes in our dynamics.
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21
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84865989755
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sloppycell
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R. N. Gutenkunst, J. C. Atlas, F. P. Casey, R. S. Kuczenski, J. J. Waterfall, C. R. Myers, and J. P. Sethna, sloppycell, http://sloppycell. sourceforge.net (2007).
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(2007)
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Gutenkunst, R.N.1
Atlas, J.C.2
Casey, F.P.3
Kuczenski, R.S.4
Waterfall, J.J.5
Myers, C.R.6
Sethna, J.P.7
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22
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34247473881
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Python unleashed on systems biology
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DOI 10.1109/MCSE.2007.60, 4160253
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C. R. Myers, R. N. Gutenkunst, and J. P. Sethna, Comput. Sci. Eng. CSENFA 1521-9615 10.1109/MCSE.2007.60 9, 34 (2007). (Pubitemid 46646863)
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(2007)
Computing in Science and Engineering
, vol.9
, Issue.3
, pp. 34-37
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Myers, C.R.1
Gutenkunst, R.N.2
Sethna, J.P.3
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23
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84865989753
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We understand this as sloppiness as arising due to the generalized interpolation argument.
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We understand this as sloppiness as arising due to the generalized interpolation argument.
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24
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0004161838
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Cambridge University Press, New York
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W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes: The Art of Scientific Computing, 3rd ed. (Cambridge University Press, New York, 2007).
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(2007)
Numerical Recipes: The Art of Scientific Computing
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Press, W.H.1
Teukolsky, S.A.2
Vetterling, W.T.3
Flannery, B.P.4
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